X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 289.0
Details 1600mM sodium citrate, Protein 51.9 mg/ml, Cryo protectant 25% ethlyene glycol, Target DB: MyabA.01244.a.A1 PS00890, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 136.35 α = 90
b = 41.18 β = 90
c = 44.97 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2011-09-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.5 68.18 99.6 0.068 -- -- -- -- 41365 -- -3.0 18.916
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.5 1.54 100.0 0.448 -- 4.37 -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.5 68.18 -- 0.0 -- 41364 2082 99.6 -- 0.1926 0.1916 0.2106 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.5 1.539 -- 147 2642 0.222 0.251 -- 99.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.4893
Anisotropic B[1][1] -0.71
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.42
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 35.047
r_dihedral_angle_4_deg 11.352
r_gen_planes_other 0.001
r_bond_other_d 0.006
r_dihedral_angle_3_deg 12.022
r_angle_other_deg 0.929
r_angle_refined_deg 1.379
r_chiral_restr 0.076
r_bond_refined_d 0.009
r_gen_planes_refined 0.006
r_dihedral_angle_1_deg 5.895
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1828
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 355

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing version: 2.3.0
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
XDS data reduction